qmake used to work perfectly with junction, as the MMP files it generated all used the (subst'd) drive that was the source of the junction. Now it appears to be able to see through the junction, and embeds the actual file name of the target of the junction into the MMP file. Since this is somewhere on c: in my case (rather than f: where my SDK and junctioned Qt git repo are) then abld barfs with lots of error messages like this:

SYSTEMINCLUDE path "\qt-s60-public\src\plugins\codecs\kr\c:\build_c\common-qt\qt-s60-public\src\plugins\codecs\kr\tmp\" not found